Contacts of the helix formed by residues 388 - 401 (chain A) in PDB entry 4U7C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A PHE* 1.3 75.4 - - - +
389A GLU* 1.3 63.9 + - - +
390A THR* 3.8 3.7 + - - -
391A SER* 3.3 7.7 + - - -
392A TRP* 2.9 25.4 + - - -
12D C 2.8 44.3 + - - -
13D G 4.9 11.9 + - - -
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A SER* 1.3 74.1 - - - +
390A THR* 1.3 58.4 + - - +
392A TRP* 3.3 18.3 - - + +
393A HIS* 2.9 66.8 + - + +
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Residues in contact with THR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A SER* 3.3 6.4 + - - -
389A GLU* 1.3 76.8 - - - +
391A SER* 1.3 57.1 + - - +
393A HIS* 3.7 5.3 - - - +
394A TYR* 2.9 31.1 + - + +
11D C 3.7 31.4 - - - +
12D C 4.2 13.0 + - - -
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Residues in contact with SER 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE* 3.9 25.4 - - - -
388A SER* 3.3 9.2 + - - -
390A THR* 1.3 80.4 - - - +
392A TRP* 1.3 57.2 + - - +
394A TYR* 3.5 7.0 + - - +
395A PHE* 2.9 40.7 + - - -
11D C 5.2 1.7 - - - -
12D C 2.5 26.4 + - - -
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Residues in contact with TRP 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 5.9 1.1 - - + -
86A VAL* 4.1 27.1 - - + -
89A PHE* 4.2 23.1 - + + -
380A ARG* 5.0 3.6 - - + +
383A LEU* 3.7 27.4 - - + +
384A SER* 3.7 28.7 + - - +
387A PHE* 3.6 11.2 - - + -
388A SER 2.9 31.2 + - - +
389A GLU* 3.3 20.7 - - + +
391A SER* 1.3 73.1 - - - +
393A HIS* 1.3 91.7 + + - +
395A PHE* 3.7 9.4 - - - +
396A LEU* 2.9 36.7 + - + +
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Residues in contact with HIS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.7 36.7 - + - -
389A GLU* 2.9 47.8 + - + +
390A THR* 3.7 6.6 - - - +
392A TRP* 1.3 115.4 - + - +
394A TYR* 1.3 62.5 + - - +
396A LEU* 3.1 6.4 + - - +
397A HIS* 2.9 36.0 + - + +
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Residues in contact with TYR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A MET* 5.7 0.3 - - - +
354A VAL* 4.2 3.3 - - - +
355A SER 2.4 33.3 + - - -
356A GLY* 3.6 8.1 - - - -
357A ILE* 3.9 22.0 - - + -
390A THR* 2.9 19.0 + - + +
391A SER* 3.5 6.5 - - - +
393A HIS* 1.3 76.6 - - - +
395A PHE* 1.3 77.1 + + - +
397A HIS* 3.0 12.7 + - + +
398A ILE* 2.9 53.3 + - + +
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ILE* 3.6 28.5 - - + -
361A THR* 3.8 19.5 - - + -
365A LEU* 3.8 24.7 - - + -
376A LEU* 3.2 36.4 - - + +
383A LEU* 4.3 22.2 - - + -
387A PHE* 4.1 26.7 - + - -
391A SER* 2.9 30.1 + - - +
392A TRP* 3.7 10.8 - - - +
394A TYR* 1.3 85.6 - + - +
396A LEU* 1.3 56.2 + - - +
398A ILE* 3.4 3.2 + - + -
399A SER* 2.9 24.8 + - - -
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 4.4 6.1 - - + +
89A PHE* 3.8 16.8 - - + -
90A ALA* 3.7 22.9 - - + +
93A LEU* 3.7 24.2 - - + -
376A LEU 5.7 0.4 - - - +
377A TYR* 4.2 20.0 - - + -
380A ARG* 4.3 23.1 - - + -
392A TRP* 2.9 27.4 + - + +
393A HIS* 3.1 5.6 + - - +
395A PHE* 1.3 74.9 - - - +
397A HIS* 1.3 65.1 + - - +
399A SER* 2.8 28.0 + - - +
400A LEU* 2.9 16.8 + - + +
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 4.7 8.7 - + - -
93A LEU* 3.6 33.2 - - + +
393A HIS* 2.9 32.7 + - + -
394A TYR* 3.4 12.7 + + + +
396A LEU* 1.3 76.1 - - - +
398A ILE* 1.3 66.8 + - + +
400A LEU* 3.3 2.2 + - - -
401A GLY 3.0 18.0 + - - -
402A LEU* 3.0 48.1 + - + +
403A GLY* 5.0 3.4 - - - -
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Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A MET* 3.9 24.8 - - + +
346A ILE* 4.0 6.9 - - - +
351A ILE* 5.8 1.1 - - + -
354A VAL* 3.8 40.6 - - + -
357A ILE* 5.7 1.3 - - + -
373A CYS* 4.0 24.1 - - - -
376A LEU* 4.1 11.9 - - + -
394A TYR* 2.9 52.2 + - + +
395A PHE* 3.5 9.2 - - + +
397A HIS* 1.3 80.1 - - + +
399A SER* 1.3 57.0 + - - +
401A GLY* 3.1 17.3 + - - -
402A LEU 5.0 1.6 - - - +
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A MET* 5.0 3.8 - - - +
346A ILE* 4.2 14.0 - - - +
373A CYS* 3.6 28.6 - - - +
376A LEU* 4.0 7.0 + - - -
377A TYR* 3.7 26.1 - - - +
395A PHE 2.9 14.9 + - - -
396A LEU* 2.8 35.2 + - - +
398A ILE* 1.3 75.6 - - - +
400A LEU* 1.3 64.0 + - - +
401A GLY 3.5 0.2 - - - -
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA* 4.0 19.3 - - + +
93A LEU* 3.9 35.2 - - + -
94A GLU* 4.3 22.7 - - + +
97A ARG* 2.7 31.0 + - - +
339A ARG* 5.7 0.7 - - - +
343A MET* 3.5 11.7 - - + +
346A ILE* 3.8 4.4 - - - +
377A TYR* 3.8 31.0 - - + -
396A LEU* 2.9 17.5 + - + +
397A HIS* 4.0 2.0 - - - +
399A SER* 1.3 82.1 - - - +
401A GLY* 1.3 59.7 + - - +
402A LEU* 3.7 14.1 - - + -
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Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 4.7 1.7 + - - -
316A ASN* 2.8 22.7 + - - -
318A MET* 3.7 10.8 - - - -
319A LEU* 3.7 8.5 - - - +
342A VAL* 4.1 7.0 - - - +
346A ILE* 3.3 21.0 - - - +
397A HIS 3.0 4.2 + - - -
398A ILE 3.1 10.3 + - - -
400A LEU* 1.3 78.3 - - - +
402A LEU* 1.3 63.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il